HorA Server Transitive Detail

Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets. J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity. Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu


Query: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.729 --> Intermediate <-- 1.467 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1uuya_) through the intermediate protein (d1efpa1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1efpa1 Large,​ alpha subunit of electron transfer flavoprotein ETFP,​ N-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1uuya_ Plant CNX1 G domainMolybdenum cofactor biosynthesis proteinsMolybdenum cofactor biosynthesis proteinsα/β

Supporting Alignments

Query <-- 0.729 --> Intermediate
DALI alignment (Z-score: 4.7 Raw score:461.40) query 1 dadeevysalvvglrayvakngfrSVLIGLS------gGIDSALVAAIACdALGAqnVYG 54 ::::::: :::::::::::: :::: ::: d1efpa1 1 ------------------------AVLLLGEvtngalnRDATAKAVAAVK-ALGD--VTV 33 query 55 VSMPSKyssDHSKGDAAELarRTGLNFRTVSiEPMFdaymaslgltglaeenlQSRL--R 112 :::::: :::::::::: :::::::::: :::: :::: : d1efpa1 34 LCAGAS--aKAAAEEAAKI--AGVAKVLVAE-DALY----------------gHRLAepT 72 query 113 GTTLMAISnQEGHIVLAPGnkselavgysTLYGDSVG----------------------- 149 :::::::: :::::::::: :::::::: d1efpa1 73 AALIVGLA-GDYSHIAAPA----------TTDAKNVMprvaalldvmvlsdvsaildadt 121 query 150 ---------------------AYGPIKDVyktsifrlaewrnraaaergqtpPIPEasit 188 :::::::: :::: d1efpa1 122 ferpiyagnaiqvvkskdakkVFTIRTAS--------------------fdaAGEG---- 157 query 189 kpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisak 248 d1efpa1 158 ----------------------------------------------------gtapvtet 165 query 249 gfgkdrrlpitnrwregh 266 d1efpa1 166 aaaadpglsswvadevae 183 FAST alignment (Normalized score: 2.23 Raw score:493.20) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGID--------SALVAAIACDALGAQ-- 50 ::::: ::::::::::: d1efpa1 1 ------------------------AVLLL------GEVTNGALNRDATAKAVAA----VK 26 query 51 ---NVYGVSMPSKYSSDH--SKGDAAELARR-TGL-NFRTVSIEPMFDAYMASLGLTGLA 103 ::::::: ::::::::::: ::: ::::::: d1efpa1 27 ALGDVTVLCA--------GASAKAAAEEAAKIAGVAKVLVAED----------------- 61 query 104 EENL------QSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDV 157 :::::::::::::::: ::::: d1efpa1 62 ----ALYGHRLAEPTAALIVGLAGDY-SHIAA---------------------------- 88 query 158 YKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGY 217 d1efpa1 89 ------------------------------------------------------------ 89 query 218 DRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----------- 266 d1efpa1 89 -------------------------------------------------PATTDAKNVMP 99 query 267 ------------------------------------------------------------ 267 d1efpa1 100 RVAALLDVMVLSDVSAILDADTFERPIYAGNAIQVVKSKDAKKVFTIRTASFDAAGEGGT 159 query 267 ------------------------ 267 d1efpa1 160 APVTETAAAADPGLSSWVADEVAE 183 TMalign alignment (TM-score: 0.34 Raw score:89.61) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGL-S----GG-IDSALVAAIACDALGAQNVYG 54 :::::: : :: ::::::::::: ::: : ::: d1efpa1 1 ------------------------AVLLLGEVTNGALNRDATAKAVAAVK-ALG-D-VTV 33 query 55 VSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSR-LRG 113 :::::: ::: :::::::: :::::::::::: :: :: ::: ::: d1efpa1 34 LCAGAS-AKA-AAEEAAKI--AGVAKVLVAEDA-LY-------------GH--RLAEPTA 73 query 114 TTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVG------------------------ 149 ::::::: ::::::::::: :: ::::: d1efpa1 74 ALIVGLA-GDYSHIAAPAT---------TD-AKNVMPRVAALLDVMVLSDVSAILDADTF 122 query 150 --------------------AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPE----- 184 :::::: : :: :: : ::: d1efpa1 123 ERPIYAGNAIQVVKSKDAKKVFTIRT-A---SF--DA---A-----------GEGGTAPV 162 query 185 ---------------------ASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVV 223 d1efpa1 163 TETAAAADPGLSSWVADEVAE--------------------------------------- 183 query 224 KTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1efpa1 184 ------------------------------------------- 184 HHsearch alignment (Probability: 0.02 E-value:0.18) query 27 LIGLSGGIDSALVAAIACDALGA--QNVYGVSMPSKYSSDHSKGDAAELARRTGLNF 81 ::::::::::::::::::::::: ::::::::: :::::::::::::::::::: d1efpa1 56 VLVAEDALYGHRLAEPTAALIVGLAGDYSHIAAP---ATTDAKNVMPRVAALLDVMV 109
Intermediate <-- 1.467 --> Hit
DALI alignment (Z-score: 4.5 Raw score:415.60) d1efpa1 1 ----AVLLLG---eVTNG-ALNRdATAKAVAAVKA------lGDVT-VLCAGasakaaae 45 :::::: :::: :::: ::::::::::: :::: ::::: d1uuya_ 1 gpeyKVAILTvsdtVSAGaGPDR-SGPRAVSVVDSsseklggAKVVaTAVVP-------- 51 d1efpa1 46 eaakiagvakvlvaedalyghRLAEPTAALIVGLA--GDYSHIAAP------atTDAKNV 97 :::::::::::::: ::::::::: :::::: d1uuya_ 52 ---------------------DEVERIKDILQKWSdvDEMDLILTLggtgftprDVTPEA 90 d1efpa1 98 MPRVAalLDVMvlsdvsaildadtfERPI--YAGNA-----iqvvkskDAKKVFTI---- 146 ::::: :::: :::: ::::: :::::::: d1uuya_ 91 TKKVI--ERET---------pgllfVMMQesLKITPfamlarsaagirGSTLIINMpgnp 139 d1efpa1 147 -RTASfdaageggtapvtetaaaadpglsswvadevae 183 :::: d1uuya_ 140 nAVAE----------------cmeallpalkhalkqik 161 FAST alignment (Normalized score: 3.76 Raw score:646.10) d1efpa1 1 ----AVLLLGEV------TNGALNRDATAKAVAAVKALGD----------VTVLCAGASA 40 ::::::: :::: ::::::::::::: ::::: d1uuya_ 1 GPEYKVAILTV-SDTVSAGAGP--DRSGPRAVSVVDS---SSEKLGGAKVVATAV----- 49 d1efpa1 41 KAAAEEAAKIAGVAKVLVAEDALYGH--RLAEPTAALIVGLA--GDYSHIAAPAT----- 91 :::::::::::::: ::::::::: d1uuya_ 50 --------------------------VPDEVERIKDILQKWSDVDEMDLILTL--GGTGF 81 d1efpa1 92 ---TDAKNVMPRVAALLD-VMVLSDVSAILDADTFER------PIYAGNAIQVVKSK--- 138 :::::::::: :::: :::: d1uuya_ 82 TPRDVTPEATKKV-----IERET--------------PGLLFVMMQE----------SLK 112 d1efpa1 139 ---------------DAKKVFTIRTASFDAAGEGGTAPVTETAAAADPGLSSWVADEVAE 183 :::::::::: d1uuya_ 113 ITPFAMLARSAAGIRGSTLIINMPG----------------------------------- 137 d1efpa1 184 ------------------------ 184 d1uuya_ 138 NPNAVAECMEALLPALKHALKQIK 161 TMalign alignment (TM-score: 0.44 Raw score:81.00) d1efpa1 1 ----AVLLLGEV-T--NGALNRDATAKAVAAVK--A-----LGDVTVLCAGASAKAAAEE 46 :::::::: : ::::::::::::::::: : ::::::::: d1uuya_ 1 GPEYKVAILTVSDTVSAGAGPDRSGPRAVSVVDSSSEKLGGAKVVATAVV---------- 50 d1efpa1 47 AAKIAGVAKVLVAEDALYGHRLAEPTAALIVGLAG--DYSHIAAPATTDA----KNVMPR 100 :::::::::::::::: :::::::: :::: :::::: d1uuya_ 51 -------------------PDEVERIKDILQKWSDVDEMDLILTL-GGTGFTPRDVTPEA 90 d1efpa1 101 VAALLDVMV--LSDVSAILDADTFERPIYAGNA----------IQVVKSKD--AKKVFTI 146 ::::::::: ::: ::::::::: ::: ::::::: d1uuya_ 91 TKKVIERETPGLLF----------VMMQESLKITPFAMLARSA-----AGIRGSTLIINM 135 d1efpa1 147 R--TAS-FD-----------------AAGEGGTAPVTETAAAADPGLSSWVADEVAE 183 : ::: :: d1uuya_ 136 PGNPNAVAECMEALLPALKHALKQIK------------------------------- 161 HHsearch alignment (Probability: 0.01 E-value:0.30) d1efpa1 70 EPTAALIVGLA--GDYSHIA 87 ::::::::::: ::::::: d1uuya_ 55 ERIKDILQKWSDVDEMDLIL 74